How to Clean a Hydroponic System Full of Algae

I’ll be the first to tell you that hydroponic gardening to grow your own food at home is both ridiculously fun and frustrating. Just when you think you’re on auto-pilot, a batch of roots clogs a pipe and sends half your plants gasping for water and you don’t know until they’re laying there lifeless one morning. Or, or, or, that harmless green fuzz surrounding your sprouts is actually a glop of green goo suffocating roots below the surface that you hadn’t checked on in a while. That there is algae and the number one reason to know how to clean a hydroponic system.

There is absolutely such a thing as beginner’s luck too. See, you set up your system and it’s pristine. It’s free of light leaks, it’s never been touched by the likes of algae and you’re adding a practically sterile grow medium to your growing unit. It will, for sure, kick-off like gangbusters, and like having a docile first child, you’ll be convinced it will be just as easy the next time around. But the second round is never the same.

For me, that’s where it gets fun (science!) but also a little frustrating. Because here’s what’s most likely to happen, because it happens to all of us after our first go-round. The winter will end, you will clean out your unit but not really clean it, and next time you use it, you’re set up for total annihilation.

Today, I’d like to help you defeat the algae that’s in your future before it makes a big ‘ol mess.

What Type of Algae is in Hydroponics?

Algae is mostly just a way of life when it comes to bigger hydroponic systems because when you combine light and water, you get algae. Since the system is pumping 16-20 hours of light a day at a system that’s circulating water from a reservoir, you’re basically farming algae.

That said, algae is more of a cosmetic and cleaning issue than a practical issue. The type of algae growing in your hydroponic system is most likely green algae, or chlorella, the same stuff you might find growing in a fish tank with a bright light.

Algae doesn’t really hurt your plants in its infancy. It’s only once it starts to gunk up your roots and deprive your plants of oxygen that you really need to start planning a good clean. Even then, you can remove pods and rinse roots as a quick fix. I certainly wouldn’t disassemble the system immediately or throw any plants out because of it until it started to really take over the system.

At that point, you’d know because it would be smelly and the algae would begin to absorb all the nutrients your plants should be getting. But if you’re cleaning your system every 3-6 months, that’s unlikely to happen, and in fact, all hydroponic systems will get some algae. But there are, of course, ways to fight back against it so you can go longer between cleans.

How to Clean a Hydroponic System if Algae is Abundant

A clean system is a happy system. If your hydroponic system has roots and a water reservoir covered in algae, now is the time to clean it.

The time not to clean it is after you’ve given up hope, let your plants die, and now you’re stuck with a dried-up system full of roots and algae dried to the wall. No, no, no friend, do not let that happen. Clean it while it’s running so you need to merely wipe, not scrub.

1. Remove your plants. If there are any you’d like to keep, you can rinse and trim the roots, then suspend them over water in a mason jar. Just use cardboard to cut out the shape of your plant vessel to hold it up. If the plants are covered in algae, I would not put them back in the spanking clean system you’re about to have.
2. Remove just your water reservoir first. Clean thoroughly with dish soap and water. Fill with 2-3 teaspoons of food-grade hydrogen peroxide per gallon of reservoir water. (Be careful with food-grade hydrogen peroxide, it’s much more potent than its drugstore counterpart, but it’s pure.)
3. Run the solution through your system. Run the water in your system for 15 minutes, so the solution can clean all the tubes and the water supply.
4. Empty the water reservoir. Rinse and re-clean the water reservoir.
5. Disassemble. Take your hydroponics system apart—I’m talking about the water reservoir and tubes, anything water runs through.
6. Hand-wash the parts with hot water and dish soap. I know it’s tempting to use the dishwasher for this part, but it won’t work and the heat can also warp the parts so they don’t fit back together as they should … and then you have no system.
7. Soak in vinegar. If you have a large sink or bucket, soak all the pieces in a solution of 1 part vinegar to 20 parts warm water, and just let soak as long as you want.
8. Replace the reservoir and run the system. Before you put any plants back in, run the water system for five minutes to dilute any hydrogen peroxide still in the lines.
9. Start your system back up, or close it down.  At this point, you can start anew, or you can leave it until next year (just don’t leave any water in the reservoir, let it dry out first.)

How to Prevent Algae in a Hydroponics System

If you are starting with a clean system, you should be fending off algae for a while, but inevitably it will eventually appear. Here’s some advice for things you can do regularly to keep algae from taking over.

• Remove and clean the water reservoir every two weeks.
• Every month on a day you’re cleaning the water reservoir, take out the plants, and run a solution of water and food-grade hydrogen peroxide through the system. Some folks use bleach, but I don’t really want any residue left in my tank. Then simply fill the water reservoir to the top with clean water, and plant food, and add the plants back.
• OR, for a less-stress approach, use drops of concentrated grapefruit seed extract at every water change (5-10 drops per gallon), which can help kill any bacteria in the tank, and in the water lines. The hydrogen peroxide approach works a lot better, but this is a lot easier and works pretty well.
• Make sure there isn’t any light getting into the tubes. It’s easy for there to be cracks in your system that are letting light in.
• Algae loves to grow on your grow medium, so when growing seedlings, cover all but the sprout itself with a wrap of tinfoil or anything light-blocking. Once the plant is large enough, you can remove it entirely because it will cover your grow medium and you won’t have to worry about it.
• Get a UV-C light for the tank that is meant for an aquarium, and do what you can to block any light the cord might be letting in, negating your efforts.
• Add a product like Hydroguard every 2 weeks (10ml), which helps break down and convert organic matter like algae into nutrients that the plants can use.

How do you keep your hydroponic system free of algae? This is the process I use, but I’d love to know your tips and techniques!